6QBX

Ovine respiratory supercomplex I+III2 closed class.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of Respiratory Supercomplex I+III2Reveal Functional and Conformational Crosstalk.

Letts, J.A.Fiedorczuk, K.Degliesposti, G.Skehel, M.Sazanov, L.A.

(2019) Mol Cell 75: 1131-1146.e6

  • DOI: https://doi.org/10.1016/j.molcel.2019.07.022
  • Primary Citation of Related Structures:  
    6Q9B, 6Q9D, 6Q9E, 6QA9, 6QBX, 6QC2, 6QC3, 6QC4, 6QC5, 6QC6, 6QC7, 6QC8, 6QC9, 6QCA, 6QCF

  • PubMed Abstract: 

    The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III 2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII 2 . CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII 2 , demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII 2 , suggesting that interaction with CI disrupts CIII 2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.


  • Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuberg 3400, Austria; Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase core protein 1A [auth a1],
K [auth a3]
446Ovis ariesMutation(s): 0 
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Find proteins for W5Q5G6 (Ovis aries)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase core protein 2B [auth a2],
L [auth a4]
439Ovis ariesMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC [auth b1],
M [auth b2]
379Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P24959 (Ovis aries)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1D [auth c1],
N [auth c2]
240Ovis ariesMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE [auth f1],
O [auth f2]
196Ovis ariesMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F [auth d1],
P [auth d2]
110Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P642 (Ovis aries)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex III subunit VIIG [auth q1],
Q [auth q2]
81Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5PUP9 (Ovis aries)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6H [auth h1],
R [auth h2]
78Ovis ariesMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRFS1NI [auth x1],
S [auth x2]
78Ovis ariesMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase, complex III subunit XJ [auth i1],
T [auth i2]
63Ovis ariesMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialU [auth V1]445Ovis ariesMutation(s): 0 
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for W5PUX0 (Ovis aries)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFV2V [auth V2]217Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5NRY1 (Ovis aries)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S1W [auth S1]704Ovis ariesMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS2X [auth S2]430Ovis ariesMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase core subunit S3Y [auth S3]228Ovis ariesMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS7Z [auth S7]179Ovis ariesMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS8AA [auth S8]176Ovis ariesMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFV3BA [auth V3]75Ovis ariesMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFS6CA [auth S6]96Ovis ariesMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit S4DA [auth S4]133Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5PE07 (Ovis aries)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A9EA [auth A9]338Ovis ariesMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2FA [auth A2]98Ovis ariesMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA5GA [auth A5]115Ovis ariesMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A6HA [auth A6]127Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5QC06 (Ovis aries)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA7IA [auth A7]112Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W5P0I2 (Ovis aries)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12JA [auth AL]145Ovis ariesMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinKA [auth AA],
VA [auth AB]
88Ovis ariesMutation(s): 0 
UniProt
Find proteins for W5NQT7 (Ovis aries)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA13LA [auth AM]143Ovis ariesMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3MA [auth D3]115Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O78753 (Ovis aries)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1NA [auth D1]318Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O78747 (Ovis aries)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6OA [auth D6]175Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LPA [auth 4L]98Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5QA [auth D5]606Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4RA [auth D4]459Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2SA [auth D2]347Ovis ariesMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA11TA [auth AK]140Ovis ariesMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B5UA [auth B5]143Ovis ariesMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8WA [auth A8]171Ovis ariesMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB10XA [auth BJ]175Ovis ariesMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialYA [auth AJ]320Ovis ariesMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit S5ZA [auth S5]105Ovis ariesMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit A3AB [auth A3]83Ovis ariesMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B3BB [auth B3]97Ovis ariesMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2CB [auth C2]120Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B4DB [auth B4]128Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB6EB [auth B6]127Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B7FB [auth B7]119Ovis ariesMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B9GB [auth B9]178Ovis ariesMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit B2HB [auth B2]72Ovis ariesMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialIB [auth B8]158Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB11JB [auth BK]125Ovis ariesMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFC1KB [auth C1]49Ovis ariesMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFB1LB [auth B1]57Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFA1MB [auth A1]70Ovis ariesMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download Ideal Coordinates CCD File 
JC [auth AK]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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BC [auth S2],
IC [auth D5]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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GC [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEC
Query on HEC

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PB [auth c1],
TB [auth c2]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
NB [auth b1],
OB [auth b1],
RB [auth b2],
SB [auth b2]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZMP
Query on ZMP

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HC [auth AA],
KC [auth AB]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN
Query on FMN

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WB [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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CC [auth S7]
DC [auth S8]
EC [auth S8]
VB [auth V1]
YB [auth S1]
CC [auth S7],
DC [auth S8],
EC [auth S8],
VB [auth V1],
YB [auth S1],
ZB [auth S1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
AC [auth S1],
QB [auth f1],
UB [auth f2],
XB [auth V2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FC [auth S6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13-2998
RECONSTRUCTIONRELION2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilAustria701309

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Other